A laboratory operated by the Centers for Disease Control and Prevention is among the handful of facilities that have secretly had their permits suspended in recent years for serious safety violations while working with bioterror pathogens, according to documents obtained by USA TODAY after winning a Freedom of Information Act appeal.

The CDC’s own labs also have been referred for additional secret federal enforcement actions six times because of serious or repeated violations in how they’ve handled certain viruses, bacteria and toxins that are heavily regulated because of their potential use as bioweapons, the CDC admitted for the first time on Tuesday. Before USA TODAY won access to records of the lab suspension, the CDC had repeatedly refused to answer questions about its own labs’ enforcement histories.

The revelations show the CDC’s facilities are among a small group of biolab operators that have the worst regulatory histories in the country, receiving repeated sanctions under federal regulations.

Citing security reasons and a federal bioterrorism law, the names of labs that have been suspended or faced other enforcement actions have been a closely guarded secret by the CDC and the U.S. Department of Agriculture. The two agencies not only operate high-security biolabs, but they also co-run the Federal Select Agent Program that regulates government, university, military and private labs that work with bioterror pathogens such as anthrax, plague and Ebola. The government calls these kinds of pathogens “select agents.”

Only five labs have been suspended from the Federal Select Agent Program since 2003 and another five labs have faced repeated referrals for enforcement actions, according to information the CDC provided last year to USA TODAY and later to congressional investigators. The revelation that CDC’s own labs are among these small groups that have faced serious and repeated sanctions raised questions among some lab safety watchdogs about the agency’s secrecy motives.

“There is no security rationale for withholding the identities of the suspended labs,” Richard Ebright, a biosafety expert at Rutgers University in New Jersey who has testified before Congress. “The sole rationale is a CYA rationale, in which the CDC seeks to cover its derriere by covering up violations and shielding staff and management responsible from accountability for violations.”

A heavily redacted USDA letter obtained by USA TODAY shows a CDC-operated lab was suspended from doing select agent research around 2007 and reinstated in 2010 because of federal violations in the handling and transfer of a virus. The USDA blacked out the name of the virus.

The CDC said Tuesday the suspension involved an individual lead scientist and the labs associated with that scientist’s research, which was located at the agency’s lab complex in Fort Collins, Colo. The violations involved research with Japanese encephalitis virus, which can cause a deadly inflammation of the brain and is often transmitted by mosquitos. As a result of the USDA inspection and findings that the research was not in compliance, the remaining samples of the virus were destroyed or transferred to another facility that was registered to possess them. The CDC noted in its statement that as of 2012, Japanese encephalitis virus was no longer considered by the federal government to be a select agent.

In response to USA TODAY’s questions about how many CDC labs have faced select agent sanctions, the CDC said its own labs have been referred six times since 2003 to the Office of Inspector General at the U.S. Department of Health and Human Services, which handles enforcement actions for select agent violations.